Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome

BMC Genomics

Methodology Article

Corinne Rouland-Lefèvre¹  David Sillam-Dussès²  Martyna Marynowska³  Philippe Delfosse³  Magdalena Calusinska³  Xavier Goux³  Yves Roisin⁴ 

[1] Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France;Institute of Research for Development - Sorbonne Universités, Institute of Ecology and Environmental Sciences - Paris, U242, 32 avenue Henri Varagnat, F-93140, Bondy, France;University Paris 13 - Sorbonne Paris Cité, Laboratory of Experimental and Comparative Ethology, EA4443, 99 avenue Jean-Baptiste Clément, F-93430, Villetaneuse, France;Luxembourg Institute of Science and Technology, 41 rue du Brill, L-4422, Belvaux, Luxembourg;Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, B-1050, Brussels, Belgium;

关键词: Carbohydrate-active enzymes (CAZymes);    Isoptera;    Metatranscriptomics;    Microbiome;    mRNA enrichment;    Termite gut;   

DOI  :  10.1186/s12864-017-4076-9

 received in 2017-03-10, accepted in 2017-08-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes. Nevertheless, several factors associated with the material sampling and library preparation steps make the metatranscriptomic studies of termite gut prokaryotic symbionts challenging.MethodsIn this study, we first examined the influence of the sampling strategy, including the whole termite gut and luminal fluid, on the diversity and the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. Secondly, we evaluated different commercially available kits combined in two library preparative pipelines for the best bacterial mRNA enrichment strategy.ResultsWe showed that the sampling strategy did not significantly impact the generated results, both in terms of the representation of the microbes and their transcriptomic profiles. Nevertheless collecting luminal fluid reduces the co-amplification of unwanted RNA species of host origin. Furthermore, for the four studied higher termite species, the library preparative pipeline employing Ribo-Zero Gold rRNA Removal Kit “Epidemiology” in combination with Poly(A) Purist MAG kit resulted in a more efficient rRNA and poly-A-mRNAdepletion (up to 98.44% rRNA removed) than the pipeline utilizing MICROBExpress and MICROBEnrich kits. High correlation of both Ribo-Zero and MICROBExpresse depleted gene expression profiles with total non-depleted RNA-seq data has been shown for all studied samples, indicating no systematic skewing of the studied pipelines.ConclusionsWe have extensively evaluated the impact of the sampling strategy and library preparation steps on the metatranscriptomic profiles of the higher termite gut symbiotic bacteria. The presented methodological approach has great potential to enhance metatranscriptomic studies of the higher termite intestinal flora and to unravel novel carbohydrate-active enzymes.

【 授权许可】

CC BY   
© The Author(s). 2017